Kaena begins as an alien ship crashes into a desert planet. Its survivors, the Vecarians, are quickly overtaken by the native Selenites. Elsewhere, a massive tree, Axis, sprouts from the core of the Vecarian ship. Time jumps six centuries ahead, where the focus shifts to the tree-dwelling humanoid, Kaena. Kaena is an inquisitive young girl who longs for adventure, a trait considered heretical by the elders. The elders demand that the tree-dwellers work for their subterranean gods.
Despite these missteps, Kaena is plagued with prophetic dreams of sunlight and water, leading her to climb the peak of Axis. It is here that Kaena meets Opaz, the last Vecarian. Opaz reveals his technology, including how he evolved worms to serve him in escaping from the planet. When Kaena mentions her dreams, Opaz begs for her help in finding Vecanoi, a memory bank of the Vecarian people. However, Vecanoi is at the very base of Axis, surrounded by the Selenites and their vengeful Queen.
Kaena's third act sees Kaena and Opaz descending ever closer to Vecanoi in the hope of reaching it before the Queen of the Selenites reach it first. Should the Queen succeed, Vecanoi will surely be destroyed.